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w3m reads the history file on startup and writes it on exit. That means if you open multiple instances of w3m, the history file will contain the history of the last instance closed. All other history changes are lost. Check if the modification time of the history file has changed before writing. If it has changed read the history file from the disk into a new history. Push the entries that are in the current history but not in the history file into the new history and write the new history to disk.
w3m: WWW wo Miru Tool ===================== w3m is a pager with WWW capability. It IS a pager, but it can be used as a text-mode WWW browser. This package is maintained for Debian <https://www.debian.org>, forked from the original version <https://sourceforge.net/projects/w3m/>. If you can read English, see doc/*. If you can read Japanese, see doc-jp/*. If you can read both, read both and correct English. :-)